Виталий

create table class (
	id int primary key auto_increment,
  	name varchar(64) unique key
);

create table subclass (
	id int primary key auto_increment,
  	class_id int references class(id),
  	name varchar(64) unique key
);

create table items (
	id int primary key auto_increment,
    subclass_id int references subclass(id),
  	name varchar(64) unique key
);

insert into class (name) values ('Fruits'), ('Vegetables');

insert into subclass (class_id, name) values (1, 'Red'), (1, 'Orange'), (2, 'Green'), (2, 'Yellow');

insert into items (subclass_id, name) values
(1, 'Apple'), (2, 'Pineapple'), (3, 'Cucumber'), (3, 'Carrot');

<?php
$query = 'select class.name class, subclass.name subclass, items.name item
from items 
join subclass on items.subclass_id = subclass.id
join class on subclass.class_id = class.id;';

// get DB version using PDO
$stmt = $pdo->prepare($query);
$stmt->execute();

$res = [];

while ($row = $stmt->fetch(PDO::FETCH_ASSOC)) {
    if (!isset($res[$row["class"]])) {
        $res[$row["class"]] = [];
    }
    if (!isset($res[$row["class"]][$row["subclass"]])) {
        $res[$row["class"]][$row["subclass"]] = [];
    }
    $res[$row["class"]][$row["subclass"]][] = $row["item"];
}

print_r(json_encode($res,  JSON_PRETTY_PRINT));